HIV infection induces strong and broadly directed, HLA class I restricted T cell responses for which specific epitopes and restricting HLA alleles have been implicated in the relative in vivo control. See Brander C, et al., Current Opinion Immunol. 2006; 18:1-8. While the bulk of the anti-viral CTL response appears to be HLA-B restricted, the relative contribution of targeted viral regions and restricting HLA molecules on the effectiveness of these responses remains obscure. See Kiepiela P, et al., Nature 2004; 432:769-775 and Ngumbela K, et al., AIDS Res. Hum. Retroviruses 2008; 24:72-82.
In addition, the role that HIV sequence diversity plays in the in vivo relevance of virus-specific T cell immunity is unclear, as functional constraints of escape variants, codon-usage at individual protein positions, T cell receptor (TCR) plasticity and functional avidity and cross-reactivity potential may all contribute to the overall effectiveness of a specific T cell response. See Brockman M, et al., J. Virol. 2007; 81: 12608-12618 and Yerly D, et al., J. Virol. 2008; 82:3147-3153. Of note, T cell responses to HIV Gag have most consistently been associated with reduced viral loads in both, HIV Glade B and Glade C infected cohorts. See Zuñiga R, et al., J. Virol. 2006; 80:3122-3125 and Kiepiela P, et al., Nat. Med. 2007; 13:46-53.
However, none of these analyses assessed the role of responses to shorter regions of the targeted protein(s) that may induce particularly effective responses. In addition, it is unclear whether the relative benefit of Gag is due to any other specific characteristic of this protein, such as expression levels, amino acid composition and inherently greater immunogenicity. It is thus feasible that protein subunits outside of Gag and within these, specific short epitope-rich regions could be identified that: i) induce responses predominantly seen in HIV controllers and ii) which would be detectable in individuals of diverse HLA types, not limited to individuals expressing alleles previously associated with effective viral control.
While some of the earlier studies have indeed controlled for a potential over-representation of Gag-derived epitopes presented on “good” HLA class I alleles, concerns remain that a purely Gag-based HIV vaccine might mainly benefit those people with an advantageous HLA genotype and will not take advantage of potentially beneficial targets outside of Gag. See Kiepiela, 2007, supra and Honeyborne I, et al., J. Virol. 2007; 81:3667-3672. In addition, CTL escape and viral fitness studies have largely been limited to Gag-derived epitopes presented in the context of relatively protective HLA alleles such as HLA-B57 and -B27. See Schneidewind A, et al., J. Virol. 2007; 81:12382-12393 and Leslie A, et al., Nat. Med. 2004; 10:282-289. The available information may thus not provide relevant information for immunogen sequences designed to protect the genetically diverse majority of the human host population.
Furthermore, many studies have focused on immunodominant targets only, despite some recent studies in HIV and SIV infection demonstrating a crucial contribution of sub-dominant responses in in vivo viral control, among them targets located outside of Gag. See Frahm N, et al., Nat. Immunol. 2006; 7:173-178 and Friedrich T, et al., J. Virol. 2007; 81:3465-3476. Together, the current view on what may constitute a protective cellular immune response to HIV is thus quite likely biased towards a focus on immunodominant responses and on responses restricted by frequent HLA class I alleles and HLA alleles associated with superior disease outcome. Therefore, the development of HIV vaccines is limited in part by the lack of immunogens capable of inducing a broad immune response. The present invention addresses the design of such immunogens.